Esempio n. 1
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 def __init__(self):
     opts = (_mapseq_lims_opt, (
         "-f", "--fasta_path",
         "Path to a directory containing a fasta file for each chromosome",
         {
             'default': None
         }
     ), ("--mincov", "Minimum coverage to call the SNP.", {
         'default': 5
     }), (
         "--minsnp",
         "Minimum percentage of reads per allele to call the SNP.", {
             'default': 40
         }
     ), ("-b", "--make_bigwigs",
         "Create genome-wide coverage, heterozygosity and quality bigwigs.",
         {
             'action': "store_true"
         }))
     usage = "[-m mapseq_minilims] [--mincov --minsnp]"
     desc = """Compares sequencing data to a reference assembly to detect SNPs."""
     Workflow.__init__(self,
                       module="snp",
                       opts=opts,
                       usage=usage,
                       desc=desc)
Esempio n. 2
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 def __init__(self):
     opts = (
         _mapseq_lims_opt,
         ("-p", "--pileup_level",
          "Target features, inside of quotes, separated by commas. E.g. 'genes,exons,transcripts'.",
          {
              'default': "genes,exons,transcripts"
          }),
         ("-j", "--junctions",
          "Whether or not to search for splice junctions using soapsplice.",
          {
              'action': "store_true",
              'default': False
          }),
         ("--stranded",
          "To indicate that the protocol was strand-specific.", {
              'action': "store_true",
              'default': False
          }),
     )
     usage = "[-m mapseq_minilims] [-p -j --stranded]"
     desc = """A High-throughput RNA-seq analysis workflow. It returns text files containing
               read counts for exons, genes and transcripts for each given BAM file, and the result
               of a DESeq run (differential expression analysis) for every pair of groups. """
     Workflow.__init__(self,
                       module="rnaseq",
                       opts=opts,
                       usage=usage,
                       desc=desc)
Esempio n. 3
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 def __init__(self):
     opts = (_mapseq_lims_opt, )
     usage = "[-m mapseq_minilims]"
     desc = """A High-throughput ChIP-seq peak analysis workflow."""
     Workflow.__init__(self,
                       module="chipseq",
                       opts=opts,
                       usage=usage,
                       desc=desc)
Esempio n. 4
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 def __init__(self):
     opts = (("--noqc", "Skip fastqc step", {'action': "store_true"}), )
     usage = "[--noqc]"
     desc = "A High-throughput sequencing data mapping workflow."
     Workflow.__init__(self,
                       module="mapseq",
                       opts=opts,
                       usage=usage,
                       desc=desc)
Esempio n. 5
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 def __init__(self):
     opts = (_mapseq_lims_opt, )
     usage = "[-m mapseq_minilims]"
     desc = """A High-throughput DNAseI-seq analysis workflow."""
     Workflow.__init__(self,
                       module="dnaseseq",
                       name="dnaseseq",
                       opts=opts,
                       usage=usage,
                       desc=desc)
Esempio n. 6
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 def __init__(self):
     opts = (_mapseq_lims_opt, )
     usage = "[-m mapseq_minilims]"
     desc = """A High-throughput microbiome analysis workflow. Will return counts per level for the selected microbiome database."""
     Workflow.__init__(self,
                       module="microbiome",
                       name="microbiome",
                       opts=opts,
                       usage=usage,
                       desc=desc)
Esempio n. 7
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 def __init__(self):
     opts = (_mapseq_lims_opt,
             ("-f", "--fasta_path", "Path to a directory containing a fasta file for each chromosome",
              {'default':None}),
             ("--mincov", "Minimum coverage to call the SNP.",
              {'default':5}),
             ("--minsnp", "Minimum percentage of reads per allele to call the SNP.",
              {'default':40}),
             ("-b","--make_bigwigs", "Create genome-wide coverage, heterozygosity and quality bigwigs.",
              {'action':"store_true"}))
     usage = "[-m mapseq_minilims] [--mincov --minsnp]"
     desc = """Compares sequencing data to a reference assembly to detect SNPs."""
     Workflow.__init__(self,module="snp",opts=opts,usage=usage,desc=desc)
Esempio n. 8
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 def __init__(self):
     opts = (_mapseq_lims_opt,
             ("-p", "--pileup_level",
              "Target features, inside of quotes, separated by commas. E.g. 'genes,exons,transcripts'.",
              {'default':"genes,exons,transcripts"}),
             ("-j", "--junctions", "Whether or not to search for splice junctions using soapsplice.",
              {'action':"store_true", 'default':False}),
             ("--stranded", "To indicate that the protocol was strand-specific.",
              {'action':"store_true", 'default':False}),
            )
     usage = "[-m mapseq_minilims] [-p -j --stranded]"
     desc = """A High-throughput RNA-seq analysis workflow. It returns text files containing
               read counts for exons, genes and transcripts for each given BAM file, and the result
               of a DESeq run (differential expression analysis) for every pair of groups. """
     Workflow.__init__(self,module="rnaseq",opts=opts,usage=usage,desc=desc)
Esempio n. 9
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 def __init__(self):
     opts = (_mapseq_lims_opt,)
     usage = "[-m mapseq_minilims]"
     desc = """A High-throughput ChIP-seq peak analysis workflow."""
     Workflow.__init__(self,module="chipseq",opts=opts,usage=usage,desc=desc)
Esempio n. 10
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 def __init__(self):
     opts = (("--noqc","Skip fastqc step",{'action':"store_true"}),
             ("--local_align","Perform local alignment",{'action':"store_true"}),)
     usage = "[--noqc] [--local_align]"
     desc = "A High-throughput sequencing data mapping workflow."
     Workflow.__init__(self,module="mapseq",opts=opts,usage=usage,desc=desc)
Esempio n. 11
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 def __init__(self):
     opts = (_mapseq_lims_opt,)
     usage = "[-m mapseq_minilims]"
     desc = """A High-throughput DNAseI-seq analysis workflow."""
     Workflow.__init__(self,module="dnaseseq",name="dnaseseq",opts=opts,usage=usage,desc=desc)
Esempio n. 12
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 def __init__(self):
     opts = (_mapseq_lims_opt,)
     usage = "[-m mapseq_minilims]"
     desc = """A High-throughput microbiome analysis workflow. Will return counts per level for the selected microbiome database."""
     Workflow.__init__(self,module="microbiome",name="microbiome",opts=opts,usage=usage,desc=desc)
Esempio n. 13
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 def __init__(self):
     desc = "Demultiplexing routine for 4C-seq data."
     Workflow.__init__(self,module="demultiplex",name="demultiplexing",desc=desc)
Esempio n. 14
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 def __init__(self):
     desc = "Demultiplexing routine for 4C-seq data."
     Workflow.__init__(self,
                       module="demultiplex",
                       name="demultiplexing",
                       desc=desc)